Use of a Managed Flow Pulse as Food Web Support for Estuarine Habitat

While freshwater inflow has been a major focus of resource management in estuaries, including the upper San Francisco Estuary, there is a growing interest in using focused flow actions to maximize benefits for specific regions, habitats, and species. As a test of this concept, in summer 2016, we used a managed flow pulse to target an ecologically important region: a freshwater tidal slough complex (Cache Slough Complex–CSC). Our goal was to improve estuarine habitat by increasing net flows through CSC to enhance downstream transport of lower trophic-level resources, an important driver for fishes such as the endangered Delta Smelt Hypomesus transpacificus. We used regional water infrastructure to direct 18.5 million m³ of Sacramento River flow into its adjacent Yolo Bypass floodplain, where the pulse continued through CSC. Simulations using a 3-D hydrodynamic model (UnTRIM) indicated that the managed flow pulse had a large effect on the net flow of water through Yolo Bypass, and between CSC and further downstream. Multiple water quality constituents (specific conductivity, dissolved oxygen, nutrients [NO₃ + NO₂, NH₄, PO₄]) varied across the study region, and showed a strong response to the flow pulse. In addition, the lower Sacramento River had increased phytoplankton biomass and improved food quality indices (estimated from long-chain essential fatty acids) after the flow pulse. The managed flow pulse resulted in increased densities of zooplankton (copepods, cladocerans) demonstrating potential advection from upper floodplain channels into the target CSC and Sacramento River regions. This study was conducted during a single year, which may have had unique characteristics; however, we believe that our study is an instructive example of how a relatively modest change in net flows can generate measurable changes in ecologically relevant metrics, and how an adaptive management action can help inform resource management.

Delivering Food to Hungry Fish in the San Francisco Estuary

The San Francisco Estuary is home to an important endangered fish called delta smelt. Delta smelt eat small, nutritious animals called zooplankton to survive and grow. In turn, zooplankton grow by eating microscopic plant-like organisms called phytoplankton. In the past, the Estuary was full of plankton and delta smelt. Because people have removed water from the Estuary and invasive species now live there, the Estuary no longer has enough plankton to feed delta smelt, making it difficult for them to survive. Scientists have found a unique place in the Estuary, the Yolo Bypass, that has lots of fish food. The problem is that delta smelt do not live in the Yolo Bypass year-round. Scientists are working to solve this problem by sending river or farm water through the Yolo Bypass, to move fish food downstream to feed the hungry delta smelt and other fish species.

Re-Examining Factors That Affect Delta Smelt (Hypomesus transpacificus) Entrainment at the State Water Project and Central Valley Project in the Sacramento–San Joaquin Delta

Managing endangered species is challenging when increased rarity leads to an inability to detect their responses to environmental conditions. In the San Francisco Estuary, the state and federally listed Delta Smelt (Hypomesus transpacificus) has declined to record low numbers, elevating concern over entrainment at the State Water Project (SWP) and Central Valley Project (CVP) water export facilities. The objective of this study was to: (1) revisit previous work on factors that affect adult Delta Smelt collected at the SWP and CVP fish collection facilities using updated conceptual models and a new statistical approach; and (2) to determine factors that affect salvage at time-scales of interest to management. Boosted Regression Tree (BRT) models were applied to salvage data at the SWP and CVP, aggregated into two response categories: a “first flush” response that represented daily salvage from the start of the entrainment window to the 50% midpoint of observed salvage, and a “seasonal” response that included daily salvage from the entire entrainment window. Precipitation, sub-adult abundance, Yolo Bypass flow, and exports best explained first flush salvage at both the SWP and CVP. The seasonal models included a similar set of influential variables, but the relative influence of precipitation was lower compared to the first flush models., Yolo Bypass flow was more influential for seasonal salvage at the SWP, compared to the CVP; Old and Middle River flow was more influential for seasonal salvage at the CVP. Although the rank of variable importance that explains salvage differed slightly between first flush and seasonal time-scales, this study suggests that salvage is most influenced by hydrodynamics, water quality, and population abundance. The application of BRT models to predict salvage is limited, because salvage has been low since federal protections were implemented in 2008. Forecast models that integrate real-time variables with fish behavior models may improve Delta Smelt management.

Re-Examining Factors that Affect Delta Smelt (Hypomesus transpacificus) Entrainment at the State Water Project and Central Valley Project in the Sacramento–San Joaquin Delta

Managing endangered species is challenging when increased rarity leads to an inability to detect their responses to environmental conditions. In the San Francisco Estuary, the state and federally listed Delta Smelt (Hypomesus transpacificus) has declined to record low numbers, elevating concern over entrainment at the State Water Project (SWP) and Central Valley Project (CVP) water export facilities. The objective of this study was to: (1) revisit previous work on factors that affect adult Delta Smelt collected at the SWP and CVP fish collection facilities using updated conceptual models and a new statistical approach; and (2) to determine factors that affect salvage at time-scales of interest to management. Boosted Regression Tree (BRT) models were applied to salvage data at the SWP and CVP, aggregated into two response categories: a “first flush” response that represented daily salvage from the start of the entrainment window to the 50% midpoint of observed salvage, and a “seasonal” response that included daily salvage from the entire entrainment window. Precipitation, sub-adult abundance, Yolo Bypass flow, and exports best explained first flush salvage at both the SWP and CVP. The seasonal models included a similar set of influential variables, but the relative influence of precipitation was lower compared to the first flush models., Yolo Bypass flow was more influential for seasonal salvage at the SWP, compared to the CVP; Old and Middle River flow was more influential for seasonal salvage at the CVP. Although the rank of variable importance that explains salvage differed slightly between first flush and seasonal time-scales, this study suggests that salvage is most influenced by hydrodynamics, water quality, and population abundance. The application of BRT models to predict salvage is limited, because salvage has been low since federal protections were implemented in 2008. Forecast models that integrate real-time variables with fish behavior models may improve Delta Smelt management.

Farm to Fish: Lessons from a Multi-Year Study on Agricultural Floodplain Habitat

Large areas of California’s historic floodplain have been separated from adjacent river channels by levee construction, allowing the development of an extensive agricultural industry. Based on successful partnerships between agriculture and conservation groups to support migrating waterfowl, we examined whether seasonally flooded rice fields could be modified to provide off-channel rearing habitat for juvenile Chinook Salmon Oncorhynchus tshawytscha. During winter and spring of 2012-2017, we conducted a series of experiments in Yolo Bypass and other regions of California’s Central Valley using hatchery Chinook Salmon as a surrogate for wild Chinook Salmon, the management target for our project. Overall, we found that seasonally flooded fields are highly productive, resulting in significantly higher levels of zooplankton and high Chinook Salmon growth rates as compared to the adjacent Sacramento River. We found similar results for multiple geographical areas in the Central Valley, and in different cover types, such as non-rice crops and fallow areas. Although field substrate type did not detectably affect fish growth and survival, connectivity with upstream and downstream areas appeared to drive fish occupancy, because rearing young salmon were generally attracted to inflow in the fields, and not all of the fish successfully emigrated off the fields without efficient drainage. In general, we faced numerous logistic and environmental challenges to complete our research. For example, periodic unmanaged floods in the Yolo Bypass made it difficult to schedule and complete experiments. During severe drought conditions, we found that managed agricultural habitats produced low and variable salmon survival results, likely because of periodically high temperatures and concentrated avian predation. In addition, our project required substantial landowner time and effort to install and maintain experimental fields. Recent and future infrastructure improvements in Yolo Bypass could substantially improve options for experimental work and broaden efforts to enhance salmon habitat.